Brig. Gen. John H. Morgan approached Cynthiana with 1,200 men, on June 11th, at dawn. Col. Conrad Garis, with the 168th Regiment Ohio Volunteer Infantry and some home guard troops, about 300 men altogether, constituted the Union forces at Cynthiana. Morgan divided his men into 3 columns, surrounded the town and launched an attack at the covered bridge, driving the Union forces back towards the depot and north along the railroad. The Confederates set fire to the town, destroying many buildings and some of the Union troops.

As the fighting flared in Cynthiana, another Union force, about 750 men of the 171st Ohio National Guard under the command of Brig. Gen. Edward Hobson, arrived by train about a mile north of the Cynthiana at Kellar's Bridge. Morgan trapped this new Union force in a meander of the Licking River.

After some fighting, Morgan forced Hobson to surrender. Altogether, Morgan had about 1,300 Union prisoners of war camping with him overnight in line of battle. Brig. Gen. Stephen Gano Burbridge with 2,400 men, a combined force of Ohio, Kentucky, and Michigan mounted infantry and cavalry, attacked Morgan at dawn on the 12th.

The Union forces drove the Confederates back, causing them to flee into town where many were captured or killed. Morgan escaped. Cynthiana demonstrated that Union numbers and mobility were starting to take their toll; Confederate cavalry and partisans could no longer raid with impunity.